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#include <cstdlib>

#include <iostream>
#include <fstream>

#include "ExtendedFASTAFileMotif.h"
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using namespace std;
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int main(int argc, char** argv) {

  String* filenameFASTAIn;
  String* filenameMotifIn;
  String* filenameOut;

  if (argc < 4) {
    cout << "Error in the input arguments. The execution must be: " << endl;
    cout << "./ExtendedFileMotif <Input fasta file> <Input Motif file> <output file>" << endl;
    return 0;
  }
  else {
    cout << "---------------------------------------------------------------------------------" << endl;
    cout << " Input Fasta File : " << argv[1] << endl;
    cout << " Input Motif File : " << argv[2] << endl;
    cout << "      Output File : " << argv[3] << endl;
    cout << "---------------------------------------------------------------------------------" << endl;
    filenameFASTAIn = new String(argv[1]);
    filenameMotifIn = new String(argv[2]);
    filenameOut     = new String(argv[3]);
  }

  ExtendedFASTAFileMotif* extendedFASTAFileMotif = new ExtendedFASTAFileMotif();

  extendedFASTAFileMotif->FilenameFASTAIn(filenameFASTAIn);
  extendedFASTAFileMotif->FilenameMotifIn(filenameMotifIn);
  extendedFASTAFileMotif->FilenameOut(filenameOut);
  
  extendedFASTAFileMotif->GetExtendedFileWithMotifSequence();

  cout << "---------------------------------------------------------------------------------" << endl;

  return 1;

}
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